- EMDB-16859: Structure of BARD1 ARD-BRCTs in complex with H2AKc15ub nucleosome... -
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Basic information
Entry
Database: EMDB / ID: EMD-16859
Title
Structure of BARD1 ARD-BRCTs in complex with H2AKc15ub nucleosomes (Map1)
Map data
Sample
Complex: BARD1 ARD-BRCTs in complex with H2AKc15ub nucleosomes
Complex: DNA, Histones and Polyubiquitin-B
DNA: DNA (142-MER)
Protein or peptide: Histone H3.1
Protein or peptide: Histone H2B type 1-C/E/F/G/I
Protein or peptide: Histone H2A type 1
Protein or peptide: Histone H4
Protein or peptide: Ubiquitin
Complex: BRCA1 associated RING domain 1
Protein or peptide: BRCA1 associated RING domain 1
Keywords
BRCA1-BARD1 / chromatin recognition / nucleosomes / ubiquitin / DNA BINDING PROTEIN
Function / homology
Function and homology information
BRCA1-BARD1 complex / BRCA1-C complex / BRCA1-B complex / BRCA1-A complex / protein K6-linked ubiquitination / regulation of phosphorylation / negative regulation of protein export from nucleus / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes ...BRCA1-BARD1 complex / BRCA1-C complex / BRCA1-B complex / BRCA1-A complex / protein K6-linked ubiquitination / regulation of phosphorylation / negative regulation of protein export from nucleus / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / heterochromatin organization / epigenetic regulation of gene expression / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Maturation of protein E / Maturation of protein E / Deposition of new CENPA-containing nucleosomes at the centromere / ER Quality Control Compartment (ERQC) / nucleosomal DNA binding / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / NOTCH2 Activation and Transmission of Signal to the Nucleus / TICAM1-dependent activation of IRF3/IRF7 / APC/C:Cdc20 mediated degradation of Cyclin B / Inhibition of DNA recombination at telomere / Meiotic synapsis / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / APC-Cdc20 mediated degradation of Nek2A / PINK1-PRKN Mediated Mitophagy / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / telomere organization / Pexophagy / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / VLDLR internalisation and degradation / Downregulation of ERBB2:ERBB3 signaling / RNA Polymerase I Promoter Opening / NF-kB is activated and signals survival / Interleukin-7 signaling / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / Translesion synthesis by POLK / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / DNA methylation / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / InlB-mediated entry of Listeria monocytogenes into host cell / IKK complex recruitment mediated by RIP1 / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / Condensation of Prophase Chromosomes / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / innate immune response in mucosa / PRC2 methylates histones and DNA / TNFR1-induced NF-kappa-B signaling pathway / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / TCF dependent signaling in response to WNT / AUF1 (hnRNP D0) binds and destabilizes mRNA / NIK-->noncanonical NF-kB signaling / Defective pyroptosis / Ubiquitin-dependent degradation of Cyclin D Similarity search - Function
Journal: Nucleic Acids Res / Year: 2023 Title: BRCA1-BARD1 combines multiple chromatin recognition modules to bridge nascent nucleosomes. Authors: Hayden Burdett / Martina Foglizzo / Laura J Musgrove / Dhananjay Kumar / Gillian Clifford / Lisa J Campbell / George R Heath / Elton Zeqiraj / Marcus D Wilson / Abstract: Chromatin association of the BRCA1-BARD1 heterodimer is critical to promote homologous recombination repair of DNA double-strand breaks (DSBs) in S/G2. How the BRCA1-BARD1 complex interacts with ...Chromatin association of the BRCA1-BARD1 heterodimer is critical to promote homologous recombination repair of DNA double-strand breaks (DSBs) in S/G2. How the BRCA1-BARD1 complex interacts with chromatin that contains both damage induced histone H2A ubiquitin and inhibitory H4K20 methylation is not fully understood. We characterised BRCA1-BARD1 binding and enzymatic activity to an array of mono- and di-nucleosome substrates using biochemical, structural and single molecule imaging approaches. We found that the BRCA1-BARD1 complex preferentially interacts and modifies di-nucleosomes over mono-nucleosomes, allowing integration of H2A Lys-15 ubiquitylation signals with other chromatin modifications and features. Using high speed- atomic force microscopy (HS-AFM) to monitor how the BRCA1-BARD1 complex recognises chromatin in real time, we saw a highly dynamic complex that bridges two nucleosomes and associates with the DNA linker region. Bridging is aided by multivalent cross-nucleosome interactions that enhance BRCA1-BARD1 E3 ubiquitin ligase catalytic activity. Multivalent interactions across nucleosomes explain how BRCA1-BARD1 can recognise chromatin that retains partial di-methylation at H4 Lys-20 (H4K20me2), a parental histone mark that blocks BRCA1-BARD1 interaction with nucleosomes, to promote its enzymatic and DNA repair activities.
Details: 20 mM HEPES pH 7.5, 50 mM NaCl and 1 mM DTT
Grid
Model: Quantifoil R3.5/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR Details: Quantifoil R3.5/1 200-mesh grids (Quantifoil Micro Tools GmbH) were glow-discharged for 30 s at 40 mA using a GloQube (Quorum) glow discharge unit
Vitrification
Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: blot force = 0 N blot time = 8 s.
Details
Purified cat BRCA1dExon11-FL BARD1 (at 3 uM) was incubated with H2AKc15ub mono-nucleosomes (at 1.5 uM) for 1 h on ice before cryo-EM grids preparation
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Electron microscopy
Microscope
FEI TITAN KRIOS
Image recording
Film or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 16015 / Average exposure time: 5.0 sec. / Average electron dose: 36.37 e/Å2
Electron beam
Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Type of model: OTHER Details: The start up model was generated directly from this dataset, following 2D Classification and Ab Initio Reconstruction in cryoSPARC 3.2.0
Final reconstruction
Number classes used: 3 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.0.1) / Number images used: 359954
Initial angle assignment
Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2.0)
Final angle assignment
Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.0.1)
Final 3D classification
Number classes: 6 / Software - Name: cryoSPARC (ver. 4.0.1)
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Atomic model buiding 1
Refinement
Space: REAL
Output model
PDB-8off: Structure of BARD1 ARD-BRCTs in complex with H2AKc15ub nucleosomes (Map1)
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